HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 21-MAR-16 5IVV TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N12 [3-((1-METHYL-1H- TITLE 2 PYRROLO[2,3-B]PYRIDIN-3-YL)AMINO)ISONICOTINIC ACID] COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LINKED KDM5A JMJ DOMAIN, UNP RESIDUES 1-87 AND 348-588; COMPND 5 SYNONYM: HISTONE DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING COMPND 6 PROTEIN 1A,RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM5A, JARID1A, RBBP2, RBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: GOLD C-PLUS KEYWDS DEMETHYLASE INHIBITION, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 3 27-SEP-23 5IVV 1 REMARK LINK REVDAT 2 03-AUG-16 5IVV 1 JRNL REVDAT 1 27-JUL-16 5IVV 0 JRNL AUTH J.R.HORTON,X.LIU,M.GALE,L.WU,J.R.SHANKS,X.ZHANG,P.J.WEBBER, JRNL AUTH 2 J.S.BELL,S.C.KALES,B.T.MOTT,G.RAI,D.J.JANSEN,M.J.HENDERSON, JRNL AUTH 3 D.J.URBAN,M.D.HALL,A.SIMEONOV,D.J.MALONEY,M.A.JOHNS,H.FU, JRNL AUTH 4 A.JADHAV,P.M.VERTINO,Q.YAN,X.CHENG JRNL TITL STRUCTURAL BASIS FOR KDM5A HISTONE LYSINE DEMETHYLASE JRNL TITL 2 INHIBITION BY DIVERSE COMPOUNDS. JRNL REF CELL CHEM BIOL V. 23 769 2016 JRNL REFN ESSN 2451-9456 JRNL PMID 27427228 JRNL DOI 10.1016/J.CHEMBIOL.2016.06.006 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.R.HORTON,A.ENGSTROM,E.L.ZOELLER,X.LIU,J.R.SHANKS,X.ZHANG, REMARK 1 AUTH 2 M.A.JOHNS,P.M.VERTINO,H.FU,X.CHENG REMARK 1 TITL CHARACTERIZATION OF A LINKED JUMONJI DOMAIN OF THE REMARK 1 TITL 2 KDM5/JARID1 FAMILY OF HISTONE H3 LYSINE 4 DEMETHYLASES. REMARK 1 REF J. BIOL. CHEM. V. 291 2631 2016 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 26645689 REMARK 1 DOI 10.1074/JBC.M115.698449 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28510 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1414 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.8841 - 3.9798 1.00 2795 139 0.1560 0.1809 REMARK 3 2 3.9798 - 3.1597 1.00 2727 139 0.1408 0.1600 REMARK 3 3 3.1597 - 2.7605 1.00 2705 147 0.1607 0.1987 REMARK 3 4 2.7605 - 2.5082 1.00 2721 145 0.1691 0.2298 REMARK 3 5 2.5082 - 2.3285 1.00 2702 138 0.1706 0.2329 REMARK 3 6 2.3285 - 2.1913 1.00 2714 139 0.1695 0.1859 REMARK 3 7 2.1913 - 2.0815 1.00 2710 135 0.1872 0.2242 REMARK 3 8 2.0815 - 1.9909 1.00 2692 150 0.1902 0.2499 REMARK 3 9 1.9909 - 1.9143 1.00 2726 127 0.2250 0.2719 REMARK 3 10 1.9143 - 1.8483 0.98 2604 155 0.2751 0.2959 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 2482 REMARK 3 ANGLE : 0.655 3405 REMARK 3 CHIRALITY : 0.046 354 REMARK 3 PLANARITY : 0.005 447 REMARK 3 DIHEDRAL : 13.977 1437 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.4592 13.9310 8.6072 REMARK 3 T TENSOR REMARK 3 T11: 0.1301 T22: 0.1099 REMARK 3 T33: 0.0585 T12: -0.0301 REMARK 3 T13: -0.0159 T23: 0.0393 REMARK 3 L TENSOR REMARK 3 L11: 2.1223 L22: 2.3065 REMARK 3 L33: 1.7442 L12: -0.0232 REMARK 3 L13: -0.0668 L23: 0.5671 REMARK 3 S TENSOR REMARK 3 S11: -0.0119 S12: -0.0445 S13: 0.0156 REMARK 3 S21: 0.0891 S22: 0.0614 S23: -0.1716 REMARK 3 S31: -0.0998 S32: 0.1497 S33: -0.0593 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.9654 19.9426 22.1406 REMARK 3 T TENSOR REMARK 3 T11: 0.2124 T22: 0.1135 REMARK 3 T33: 0.1207 T12: 0.0519 REMARK 3 T13: 0.0389 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 2.5148 L22: 2.8484 REMARK 3 L33: 3.5196 L12: 1.9616 REMARK 3 L13: 0.5175 L23: 0.5338 REMARK 3 S TENSOR REMARK 3 S11: -0.0259 S12: -0.1383 S13: 0.1606 REMARK 3 S21: 0.3813 S22: -0.0015 S23: 0.1357 REMARK 3 S31: -0.0692 S32: -0.1992 S33: 0.0250 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 406 THROUGH 469 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4025 21.8316 5.4952 REMARK 3 T TENSOR REMARK 3 T11: 0.1889 T22: 0.2437 REMARK 3 T33: 0.2237 T12: -0.0902 REMARK 3 T13: 0.0283 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 2.5981 L22: 1.1647 REMARK 3 L33: 0.5892 L12: -1.2035 REMARK 3 L13: -0.5391 L23: 0.4869 REMARK 3 S TENSOR REMARK 3 S11: 0.0441 S12: -0.0633 S13: 0.2850 REMARK 3 S21: -0.0406 S22: 0.0661 S23: -0.2652 REMARK 3 S31: -0.2900 S32: 0.3625 S33: -0.0744 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 470 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.7600 14.6484 3.6384 REMARK 3 T TENSOR REMARK 3 T11: 0.0981 T22: 0.0561 REMARK 3 T33: 0.0882 T12: 0.0007 REMARK 3 T13: 0.0148 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.4155 L22: 1.3551 REMARK 3 L33: 2.2861 L12: -0.0718 REMARK 3 L13: 0.3414 L23: 0.3245 REMARK 3 S TENSOR REMARK 3 S11: -0.0087 S12: 0.0497 S13: -0.0220 REMARK 3 S21: -0.0157 S22: -0.0041 S23: 0.0862 REMARK 3 S31: -0.0815 S32: -0.0521 S33: 0.0076 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5IVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219523. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6-9.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28515 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.848 REMARK 200 RESOLUTION RANGE LOW (A) : 32.879 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5E6H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2-1.35 M (NH4)2SO4, 0.1 M TRIS-HCL REMARK 280 (PH 8.6-9.2) 0-20% GLYCEROL 25 MM (NA/K) DIBASIC/MONOBASIC REMARK 280 PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 58.12400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.13950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.12400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.13950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 918 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 930 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A -1 REMARK 465 ASN A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 VAL A 4 REMARK 465 GLY A 5 REMARK 465 PRO A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 8 REMARK 465 TYR A 9 REMARK 465 ALA A 10 REMARK 465 ALA A 11 REMARK 465 THR A 344 REMARK 465 ARG A 345 REMARK 465 VAL A 346 REMARK 465 ARG A 347 REMARK 465 PRO A 348 REMARK 465 ARG A 349 REMARK 465 GLU A 350 REMARK 465 ALA A 457 REMARK 465 HIS A 458 REMARK 465 ILE A 459 REMARK 465 ASN A 460 REMARK 465 VAL A 461 REMARK 465 ASP A 462 REMARK 465 ILE A 463 REMARK 465 SER A 464 REMARK 465 GLY A 465 REMARK 465 MET A 466 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 ARG A 69 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 GLN A 356 CG CD OE1 NE2 REMARK 470 VAL A 358 CG1 CG2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 LYS A 392 CG CD CE NZ REMARK 470 ILE A 401 CG1 CG2 CD1 REMARK 470 GLU A 402 CG CD OE1 OE2 REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 LYS A 425 CG CD CE NZ REMARK 470 ARG A 428 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 430 CG CD CE NZ REMARK 470 GLU A 452 CG CD OE1 OE2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 SER A 454 OG REMARK 470 VAL A 455 CG1 CG2 REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 GLN A 513 CG CD OE1 NE2 REMARK 470 ARG A 519 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 524 CG CD OE1 OE2 REMARK 470 GLU A 527 CG CD OE1 OE2 REMARK 470 LEU A 532 CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 882 O HOH A 953 4455 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 477 -7.61 81.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 990 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 991 DISTANCE = 6.28 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 483 NE2 REMARK 620 2 GLU A 485 OE1 96.4 REMARK 620 3 HIS A 571 NE2 84.3 87.0 REMARK 620 4 6EN A 601 N07 87.7 169.7 102.8 REMARK 620 5 HOH A 736 O 93.0 79.7 166.1 90.7 REMARK 620 6 HOH A 852 O 174.6 89.0 96.7 86.9 87.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6EN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ISL RELATED DB: PDB REMARK 900 RELATED ID: 5IVB RELATED DB: PDB REMARK 900 RELATED ID: 5IVC RELATED DB: PDB REMARK 900 RELATED ID: 5IVE RELATED DB: PDB REMARK 900 RELATED ID: 5IVF RELATED DB: PDB REMARK 900 RELATED ID: 5IVJ RELATED DB: PDB REMARK 900 RELATED ID: 5IVY RELATED DB: PDB REMARK 900 RELATED ID: 5IW0 RELATED DB: PDB REMARK 900 RELATED ID: 5IWF RELATED DB: PDB DBREF 5IVV A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 5IVV A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 5IVV HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 5IVV ASN A 0 UNP P29375 EXPRESSION TAG SEQRES 1 A 330 HIS ASN MET ALA GLY VAL GLY PRO GLY GLY TYR ALA ALA SEQRES 2 A 330 GLU PHE VAL PRO PRO PRO GLU CYS PRO VAL PHE GLU PRO SEQRES 3 A 330 SER TRP GLU GLU PHE THR ASP PRO LEU SER PHE ILE GLY SEQRES 4 A 330 ARG ILE ARG PRO LEU ALA GLU LYS THR GLY ILE CYS LYS SEQRES 5 A 330 ILE ARG PRO PRO LYS ASP TRP GLN PRO PRO PHE ALA CYS SEQRES 6 A 330 GLU VAL LYS SER PHE ARG PHE THR PRO ARG VAL GLN ARG SEQRES 7 A 330 LEU ASN GLU LEU GLU ALA MET THR ARG VAL ARG PRO ARG SEQRES 8 A 330 GLU ALA PHE GLY PHE GLU GLN ALA VAL ARG GLU TYR THR SEQRES 9 A 330 LEU GLN SER PHE GLY GLU MET ALA ASP ASN PHE LYS SER SEQRES 10 A 330 ASP TYR PHE ASN MET PRO VAL HIS MET VAL PRO THR GLU SEQRES 11 A 330 LEU VAL GLU LYS GLU PHE TRP ARG LEU VAL SER SER ILE SEQRES 12 A 330 GLU GLU ASP VAL ILE VAL GLU TYR GLY ALA ASP ILE SER SEQRES 13 A 330 SER LYS ASP PHE GLY SER GLY PHE PRO VAL LYS ASP GLY SEQRES 14 A 330 ARG ARG LYS ILE LEU PRO GLU GLU GLU GLU TYR ALA LEU SEQRES 15 A 330 SER GLY TRP ASN LEU ASN ASN MET PRO VAL LEU GLU GLN SEQRES 16 A 330 SER VAL LEU ALA HIS ILE ASN VAL ASP ILE SER GLY MET SEQRES 17 A 330 LYS VAL PRO TRP LEU TYR VAL GLY MET CYS PHE SER SER SEQRES 18 A 330 PHE CYS TRP HIS ILE GLU ASP HIS TRP SER TYR SER ILE SEQRES 19 A 330 ASN TYR LEU HIS TRP GLY GLU PRO LYS THR TRP TYR GLY SEQRES 20 A 330 VAL PRO SER HIS ALA ALA GLU GLN LEU GLU GLU VAL MET SEQRES 21 A 330 ARG GLU LEU ALA PRO GLU LEU PHE GLU SER GLN PRO ASP SEQRES 22 A 330 LEU LEU HIS GLN LEU VAL THR ILE MET ASN PRO ASN VAL SEQRES 23 A 330 LEU MET GLU HIS GLY VAL PRO VAL TYR ARG THR ASN GLN SEQRES 24 A 330 CYS ALA GLY GLU PHE VAL VAL THR PHE PRO ARG ALA TYR SEQRES 25 A 330 HIS SER GLY PHE ASN GLN GLY TYR ASN PHE ALA GLU ALA SEQRES 26 A 330 VAL ASN PHE CYS THR HET 6EN A 601 20 HET MN A 602 1 HETNAM 6EN 3-[(1-METHYL-1H-PYRROLO[2,3-B]PYRIDIN-3-YL) HETNAM 2 6EN AMINO]PYRIDINE-4-CARBOXYLIC ACID HETNAM MN MANGANESE (II) ION FORMUL 2 6EN C14 H12 N4 O2 FORMUL 3 MN MN 2+ FORMUL 4 HOH *291(H2 O) HELIX 1 AA1 GLU A 27 THR A 30 5 4 HELIX 2 AA2 ASP A 31 GLU A 44 1 14 HELIX 3 AA3 LEU A 363 ASN A 379 1 17 HELIX 4 AA4 PRO A 381 VAL A 385 5 5 HELIX 5 AA5 PRO A 386 SER A 400 1 15 HELIX 6 AA6 SER A 415 GLY A 419 1 5 HELIX 7 AA7 LEU A 432 GLU A 434 5 3 HELIX 8 AA8 GLU A 435 SER A 441 1 7 HELIX 9 AA9 ASN A 444 MET A 448 5 5 HELIX 10 AB1 GLU A 485 SER A 489 5 5 HELIX 11 AB2 PRO A 507 HIS A 509 5 3 HELIX 12 AB3 ALA A 510 ALA A 522 1 13 HELIX 13 AB4 PRO A 523 GLU A 527 5 5 HELIX 14 AB5 PRO A 530 GLN A 535 1 6 HELIX 15 AB6 ASN A 541 HIS A 548 1 8 SHEET 1 AA1 8 VAL A 21 PHE A 22 0 SHEET 2 AA1 8 ILE A 48 ILE A 51 1 O LYS A 50 N PHE A 22 SHEET 3 AA1 8 PHE A 562 THR A 565 -1 O PHE A 562 N ILE A 51 SHEET 4 AA1 8 TYR A 490 GLY A 498 -1 N ASN A 493 O VAL A 563 SHEET 5 AA1 8 ASN A 579 PHE A 586 -1 O GLU A 582 N TYR A 494 SHEET 6 AA1 8 TRP A 470 GLY A 474 -1 N TRP A 470 O ALA A 583 SHEET 7 AA1 8 ILE A 406 SER A 414 -1 N ILE A 413 O LEU A 471 SHEET 8 AA1 8 ARG A 73 ARG A 76 -1 N GLN A 75 O VAL A 407 SHEET 1 AA2 2 ARG A 69 PHE A 70 0 SHEET 2 AA2 2 TYR A 361 THR A 362 -1 O TYR A 361 N PHE A 70 SHEET 1 AA3 4 SER A 479 HIS A 483 0 SHEET 2 AA3 4 HIS A 571 ASN A 575 -1 O GLY A 573 N PHE A 480 SHEET 3 AA3 4 LYS A 501 GLY A 505 -1 N THR A 502 O PHE A 574 SHEET 4 AA3 4 TYR A 553 GLN A 557 -1 O GLN A 557 N LYS A 501 LINK NE2 HIS A 483 MN MN A 602 1555 1555 2.23 LINK OE1 GLU A 485 MN MN A 602 1555 1555 2.16 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.35 LINK N07 6EN A 601 MN MN A 602 1555 1555 2.20 LINK MN MN A 602 O HOH A 736 1555 1555 2.29 LINK MN MN A 602 O HOH A 852 1555 1555 2.13 SITE 1 AC1 13 ARG A 73 TYR A 409 ASP A 412 TYR A 472 SITE 2 AC1 13 PHE A 480 HIS A 483 LYS A 501 TRP A 503 SITE 3 AC1 13 HIS A 571 MN A 602 HOH A 840 HOH A 852 SITE 4 AC1 13 HOH A 868 SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 6EN A 601 SITE 2 AC2 6 HOH A 736 HOH A 852 CRYST1 116.248 62.279 46.592 90.00 92.46 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008602 0.000000 0.000370 0.00000 SCALE2 0.000000 0.016057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021483 0.00000